In base R

At this point, I’m going to move ahead to plots, before coming back to other ways to manipulate data frames. The reason is simple: plotting my data is usually my first pass at seeing what’s going on. I usually manipulate my data frames for the purpose of plotting it in a particular way, and seeing the data first gives me better ideas of how to manipulate the data frame in order to plot it more informatively.

For the hs_sorted data, one question we might ask is how socioeconomic status affects test scores. A boxplot will start to answer this question informatively. In base R, we use the function boxplot() to do this. In this function, we see a new character ~. We read this as “by”. The function below can be read as “make a plot of how the test score value varies by socioeconomic status. Use hs_sorted as the data”.

boxplot(value ~ ses, data = hs_sorted)

This is a nice first pass at the data. We learn that test scores go up for higher SES scores. Other plot commands in base R include:

Function Does
boxplot(y ~ x, data = data_frame) boxplot
plot(y ~ x, data = data_frame) scatter plot
hist(data_frame$column) histogram
density(data_frame$column) density plot

For a detailed look at graphics in base R, check out Joe’s R Study Group.

Making it nice with ggplot

I find R’s base plots actually much harder to deal with than ggplot (which stands for “graphics of grammar plot”), since base plots are hard to control - so my first step in looking at data is actually to plot it using ggplot. Today, I’ll introduce ggplot, and tomorrow we’ll go into more detail.

ggplot is a package that give you a lot of freedom over your plots. Its defaults are set to make beautiful plots, which - let’s face it - makes it easier to convince people that your data is the real deal. My go-to for help with ggplot is Winston Chang’s Cookbook for R. Again, Joe’s R Study Group is also a great tutorial, and Hadley Wickham’s (the author of ggplot) paper on ggplot provides some more in-depth info on the theory behind ggplot as a data visualization tool. I especially recommend reading Section 7 (just one page long) Here’s a teaser:


How can we build on top of the grammar to help data analysts build compelling, revealing graphics? What would a poetry of graphics look like?


Who doesn’t want their graphics to be compelling and revealing - poetic in their informativeness!? I’m sold. ggplot works a little differently than plotting in base R, because it’s not just a single line of code.

With ggplot, you’re creating a plot out of layers. The main types of layers that you’ll add are:


Let’s try it out!

We’ll start with the ggplot equivalent of the boxplot that we made above in base graphics. First we need to install and load ggplot2.

install.packages("ggplot2")
library(ggplot2)
## 
## Attaching package: 'ggplot2'
## 
## The following object is masked _by_ '.GlobalEnv':
## 
##     movies
head(hs_sorted)
##     id female race ses schtyp prog variable value
## 99   1      1    1   1      1    3     read    34
## 299  1      1    1   1      1    3    write    44
## 499  1      1    1   1      1    3     math    40
## 699  1      1    1   1      1    3  science    39
## 899  1      1    1   1      1    3    socst    41
## 139  2      1    1   2      1    3     read    39

The basic way to create a plot is to put the data and aesthetics in the ggplot() function, and then add the layers of geom and stat that you want. The first line calls the data frame as the first argument, and then the list of aesthetic mappings as the second argument.

ggplot(data_frame, aes(x = x_var, y = y_var))

After adding the data, we can make that data materialize with whatever geometric layer we want. We achieve this by adding a + to the end of the first line, so that the function knows its not done yet. Most style guides will suggest adding each layer on its own line, to keep the code maximally readable.

ggplot(hs_sorted, aes(x = ses, y = value)) +
  geom_boxplot()

Something’s wrong here … Why is ggplot only giving us one overall boxplot instead of a separate boxplot for each ses? The answer has to do with how the data is coded. If we take a look at the summary of hs_sorted, we can see that R thinks that ses is a measurement on a scale. It tells us that 2.055 is the mean socioeconomic status of this dataset. But this is silly: we know that students are given a discrete score of either 1, 2, or 3. In other words, even though ses is represented as a numeric variable, it’s actually a factor variable. It increases in discrete steps.


summary(hs_sorted)
##        id             female           race           ses       
##  Min.   :  1.00   Min.   :0.000   Min.   :1.00   Min.   :1.000  
##  1st Qu.: 50.75   1st Qu.:0.000   1st Qu.:3.00   1st Qu.:2.000  
##  Median :100.50   Median :1.000   Median :4.00   Median :2.000  
##  Mean   :100.50   Mean   :0.545   Mean   :3.43   Mean   :2.055  
##  3rd Qu.:150.25   3rd Qu.:1.000   3rd Qu.:4.00   3rd Qu.:3.000  
##  Max.   :200.00   Max.   :1.000   Max.   :4.00   Max.   :3.000  
##      schtyp          prog          variable       value      
##  Min.   :1.00   Min.   :1.000   read   :200   Min.   :26.00  
##  1st Qu.:1.00   1st Qu.:2.000   write  :200   1st Qu.:45.00  
##  Median :1.00   Median :2.000   math   :200   Median :52.50  
##  Mean   :1.16   Mean   :2.025   science:200   Mean   :52.38  
##  3rd Qu.:1.00   3rd Qu.:2.250   socst  :200   3rd Qu.:61.00  
##  Max.   :2.00   Max.   :3.000                 Max.   :76.00


Factors are actually a litte complicated. Underlyingly, they are numeric values that are represented with character strings. This mostly has implications for statistical analysis, which we won’t be getting into in this mini course. But it’s good to know that when you have e.g, gender represented as a factor (which is R’s default representation for character variables), it is underlying a series of 0 and 1.

For the purpose of plotting the data in an informative way, all we need to do is realize that the ses variable looks linear to ggplot, but that we intend it to be a factor. Easy! We can coerce variables into other data types by using the following:

Function Does
as.factor() coerce to factor
as.character() coerce to character string
as.numeric() coerce to numbers

For this data, we need to coerce ses to a factor. We can do this either outside of the ggplot function or within it. The following are equivalent:

## change the data frame and then plot it (good for if you want to continue working with ses as a factor) 

hs_sorted$ses <- as.factor(hs_sorted$ses) 
ggplot(hs_sorted, aes(x = ses, y = value)) +
  geom_boxplot()

## change the variable just when you plot it
ggplot(hs_sorted, aes(x = as.factor(ses), y = value)) +
  geom_boxplot()

Both of these options produce the graph we’re looking for:

More ways to visualize with ggplot


Okay great, so we made the same graph as before, and it looks a little bit nicer. But we’re just getting started! One of the biggest benefits of using ggplot as a first pass at your data is the flexible aesthetics. With ggplot, we can assign color or shape based on a variable - which is something we can’t do in base R1 that takes an extra step to do in base R.

Let’s see whether gender has an additional effect on test scores. Note that the gender variable gives us the same problem as the socioeconomic status variable, so we have to also coerce it to a factor first.

ggplot(hs_sorted, aes(x = ses, y = value, color = as.factor(female))) + 
  geom_boxplot()

Beautiful! What else might be informative? Maybe there’s a difference in subject score by socioeconomic status, or by gender? Note that here I’m also changing the color aesthetic mapping to a fill, because I want the boxes to be filled with color instead of just changing the color of the lines.

ggplot(hs_sorted, aes(x = variable, y = value, fill = ses)) + 
  geom_boxplot() 

ggplot(hs_sorted, aes(x = variable, y = value, fill = as.factor(female))) +
  geom_boxplot()

Arguments and Layers

Below is a list of some of the aesthetic options, geoms, stat layers, and fine-tuning arguments that I use regularly. This is not a full list! (see ggplot documentation) for a current list of layers supported by ggplot.

Some of the levels need specified arguments (see, e.g. geom_boxplot, which usually needs stat = "identity", for most data types). R is great at letting you know when you need to specify an argument, so there’s no risk in trying a level. If you haven’t given ggplot all the info it needs, it’ll tell you what to add.

Aesthetic arguments

Argument Does
x = assigns variable to x. Not optional.
y = assigns variable to y
color = assigns color of lines or points. Note that colour = also works
fill = assigns the fill of 2-dimensional shapes
size = assigns size (of points or line width)
shape = assigns shape
alpha = assigns transparency
linetype = assigns line type
label = assigns text (for use with geom_text())

Geometric levels

Geom Makes
geom_point() scatterplot
geom_bar(stat = "identity") barplot
geom_boxplot() boxplot
geom_violinplot() violin plot
geom_line() line plot (connects points left to right)
geom_path() line plot (connects points in the order they appear in the data frame)
geom_area() area plot (filled in from line to x axis)
geom_text() scatterplot of text
geom_blank() draws a blank layer. Unclear why this exists.
geom_contour() contour plot
geom_histogram() histogram
geom_errorbar() error bars
geom_jitter() points - jittered (to reduce overlap)

Statistic levels

Stat Does
stat_smooth() smoothed line
stat_density() density plot
stat_summary() summarize y value for each x

Scale assignment

Scale Does
scale_alpha() set alpha range
scale_area() scale area instead of radius for size aesthetic
scale_color_gradient() smooth gradient bewteen two colors
scale_color_grey() gray scale
scale_manual() set alpha, color, fill, linetype, shape, size, manually
scale_linetype() set linetype scale
scale_size() set size range
scale_x() adjust x: reverse it, put in log space,

Labels and themes

Function Does
labs() add title, x axis, y axis, legend titles
xlim() change limits of x axis
ylim() change limits of y axis
theme_bw() white background, black gridlines
theme_grey() grey background, white gridlines
theme() set theme elements (text size, linetype, etc.)


An example with the hs_sorted data

ggplot(hs_sorted, aes(x = ses, y = value, fill = as.factor(female))) +
  geom_boxplot() +
  labs(x = "\nSocioeconomic Status", y = "Test Scores\n", fill = "Gender", title = "Test scores by Gender and SES\n") + 
  scale_fill_brewer(breaks = c(0, 1),
                    labels = c("Male", "Female")) + 
  scale_x_discrete(breaks = c(1, 2, 3),
                   labels = c("Lower", "Middle", "Upper")) +
  theme_bw()

  1. Thanks to Daniel Ezra Johnson for pointing this out!↩